TRIPOLI, Libya (AP) — One of Libya’s highest military officers resigned Sunday after clashes between protesters and a government-aligned militia he was in charge of left 31 people dead in the eastern city of Benghazi, the deadliest such violence in a country where armed factions hold sway.

The bloodshed underscored the growing public anger over the government’s failure to build an army capable of reining in the militias that dominate parts of the country nearly two years after the fall of Moammar Gadhafi. The militias have become bolder in trying to shape Libya’s politics.

The violence erupted Saturday when protesters in Benghazi, the country’s second largest city, stormed the main camp of Libya Shield, a largely Islamist grouping of militias that are paid by the government to help maintain security. The protesters were demanding that the militias submit to the full authority of Libya’s security forces or lay down their arms.

The clashes prompted Army Chief of Staff Maj. Gen. Youssef al-Mangoush to resign, citing the unusually high death toll from the violence. Al-Mangoush was due to be replaced soon, and the country’s Congress voted in support of accepting his resignation Sunday.

He was in charge of the country’s roughly 12 Libya Shield brigades, tasked with putting them on government payroll and directing them.

The brigades, though sanctioned by the state, operate as a parallel security structure to the country’s police and armed forces. Libya Shield members are neither entirely under the authority of the state nor operating entirely renegade.

Libya’s nascent police and military rely on the brigades to help with security of the country. The militias are rooted in the brigades of rebels who fought to oust Gadhafi in the 2011 uprising against the longtime leader. They have since mushroomed in power and size as the government continues to struggle to build its security forces after the civil war.

In the weeks leading up to Saturday’s incident, military officers had been protesting al-Mangoush, accusing him of corruption and of failing to exert authority over militias. Some militias were believed to have favored al-Mangoush remaining in his post, because he had been unable or possibly unwilling to replace them with a strong unified force.

The militias, many of them refusing to join the army until ministries are purged of former regime officials, are seen by some as exhibiting too much autonomy, according to Frederic Wehrey of the Carnegie Endowment for International Peace.

“Local residents are upset from the sort-of parasitic nature of these militias,” said Wehrey, who was recently in Benghazi. “I think some of these Shield forces were trying to help police the east, but were leveraging their firepower to try and get concessions from the government.”

Benghazi, the birthplace of the revolution that led to Gadhafi’s capture and killing, was the site of the Sept. 11 assault last year on the U.S. diplomatic mission that killed Ambassador Chris Stevens and three other Americans. High level police officials have also been assassinated and security bases have come under frequent attack there by unidentified assailants.

In Saturday’s clashes, witnesses said hundreds of protesters — some of the armed — marched on the Libya Shield’s base, apparently outnumbering the militiamen inside.

It remains unclear which side fired first in Saturday’s incident. Libyan officials have provided few details of the clashes.

Yousef Abdel-Salam, who joined the rally Saturday but left after gunshots were fired, told The Associated Press the protest was meant to support the army and police as the country’s sole security bodies.

Video taken by activists and posted on social media websites showed people firing machine guns mounted on the backs of pick-up trucks during the clashes. Some were seen ducking for cover behind trees and cars, while others ferried the wounded to ambulances. The footage appeared genuine and conformed with independent witness reports of the events.

Hospital officials said protesters made up most of 31 dead. The officials spoke anonymously as they were not authorized to speak to reporters.

According to the director at the city’s Jalaa Hospital Mohamed Belied, the deaths were caused by gunshots and explosive fragments. He said that dozens of people were wounded.

Among the dead were five members of the military’s special forces, known as the “Saaqa,” who were killed by an explosion when their forces tried to move in on the base, Col. Abdullah el-Shiafy said, according to the official Libyan News Agency LANA. Ten others in the force were wounded.

On Sunday, Saaqa troops controlled the main Libya Shield base where the clashes took place. Other security units took control of the remaining three Libya Shield camps in the city, according to el-Shiafy.

The head of Libya Shield in Benghazi, Wassim Bin Hamid, told a local radio station that those behind the assault were supporters of a campaign to declare eastern Libya an autonomous federal state and that they were aiming to create strife.

Benghazi security official Abdel-Salam al-Barghathi told The Associated Press that protesters were simply fed up with the militias, which he said do not take orders from anyone.

Militias have been increasingly exerting their power for political gains — most notably in the lead-up to the passage last month of a contentious law that bans Gadhafi-era officials from senior government posts for 10 years.

Bin Hamid, of Benghazi’s Libya Shield force, was among those pushing for the law. He helped direct militias who lay siege to government buildings in the capital demanding the bill’s passage.

Mohammed al-Megarif, the former head of the General National Congress, suggested in his resignation speech last month that lawmakers had used militias to pressure passage of the bill. The Gadhafi-era ambassador, who defected years ago to lead the opposition in exile, decried what he described as the empowerment of some legislators backed by gunmen.

Libya’s Muslim Brotherhood was among the parties that rallied successfully to pass the law in the face of liberal opposition.

While Saturday’s incident was the most violent involving anti-militia protesters, it was not the first. Last September, after the U.S. ambassador was killed, hundreds of people attacked the offices of an Islamist militia forcing its dissolution. No deaths were reported then.

Benghazi’s volatile security situation has prompted a renewed push for self-rule in the east. Many residents of the east blame the central government for failing to clamp down on a proliferation of weapons from the 2011 civil war. They complain of discrimination by the west, where the capital, Tripoli, is located.

Prime Minister Ali Zidan, in a statement issued early Sunday, acknowledged that the large number of weapons in the east “led to what happened.” He also urged people to show self-restraint, suggesting his government would not be immediately taking a tough stance against the state-sanctioned militias.

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